rs191986791
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_015443.4(KANSL1):c.1857G>T(p.Arg619=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,607,270 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R619R) has been classified as Likely benign.
Frequency
Consequence
NM_015443.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KANSL1 | NM_015443.4 | c.1857G>T | p.Arg619= | synonymous_variant | 7/15 | ENST00000432791.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KANSL1 | ENST00000432791.7 | c.1857G>T | p.Arg619= | synonymous_variant | 7/15 | 1 | NM_015443.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000926 AC: 23AN: 248366Hom.: 0 AF XY: 0.0000820 AC XY: 11AN XY: 134114
GnomAD4 exome AF: 0.000144 AC: 209AN: 1455112Hom.: 1 Cov.: 30 AF XY: 0.000143 AC XY: 103AN XY: 722620
GnomAD4 genome AF: 0.000125 AC: 19AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 29, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | KANSL1: BP4, BP7 - |
Koolen-de Vries syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at